# PhD Prep¶

## Tuesday 22 March¶

So, I’m not currently enrolled and I’ve not received an offer yet as the graduate research office is inundated with paperwork atm, but I am going to start anyway as my commencement date was yesterday. I came in though and the only really did a few clerical things and taught for the afternoon (god it felt good to be back int he teaching labs ), but after a quick chat with Peter I think I know what I need to be doing…

It’s such a mammoth task to think about I feel like a decent methodology would be to:

1. Start by reviewing my honours thesis
• Go over the IL notes that I put aside when my project pivoted
• Review some key papers that I identified in that work
2. Start exploring the field more broadly
• What are the papers that I didn’t get around to properly digesting?
• What are some larger reviews that I really need to have read?
• I have a big pile of papers in my “to read” list that I should probably down
3. To try and read more broadly as well to get a more diverse understanding of the field

I really need to find a good way to be able to keep track of notes though as this is going to explode in detail so much. Perhaps I need a structure on this website to deal with that

#### What I actually did:¶

• Chatted, got into the groove of things and decided to switch from Mendeley to Zotero for organisational reasons
• Comment from Katya:

“At the moment you need to focus on literature covering the prediction of kinetics from MD simulations or ab initio MD simulations.”

## Wednesday 23 March¶

#### What I actually did:¶

• Today I really just focused on the CHM3911 tutorial and prep. I did also set up a self hosted WebDav server on my little NUC in order to save myself \$20 USD on the Zotero storage access, which was ultimately decided by experiencing how incredibly slow Zotero’s paper storage is. Simply put, I can’t justify spending that money to wait for minutes for a 3 MB paper to download.

## Friday 1 April¶

Error

Well, It looks like the direction for my PhD has changed drastically after a chat with Katya, which means that I’m starting from scratch.

### Meeting Notes¶

• Lit review should be no more than 15 pages and the talk should be max 20 mins with a goal of 15 mins. These should focus on snippets of what is already out there in the field.
• After much back and forth the new project is going to be something relating to better handling of solvation for UV-vis/Fluorescence spectroscopic predictions by utilising multilayered computational approaches

• Could potentially involve a mix of QM/QM/SE/MM or any combination of theories to better model the solvent effects.
• In contrast to the previous project, this will be far more focused on the application of pre-existing methodologies in new ways, as opposed to the creation of all new methods.
• Potential search terms:

• Excited state calculations
• UV-Vis spectroscopic methods (QM, MD, etc.)
• Predicting these in solvent (explicit, implicit, QM/MM)
• Chromophores/fluorophores
• Potential investigation; Green Fluorescent Protein (GFP)

• What stops people from predicting chromophores and fluoropohres of interest?
• What systems do they want to be able to predict? (avoid NDIs…)
• Researchers of interest:

The new project will likely be looking into something along the lines of multilayered (ONIOM-like) approaches to try and better account for solvent effects in excited state calculations, probably for better/more robust determination of fluorosence spectroscopy. This is going to take a lot of reading to get my head around...